Suppression of electrophoretic anomaly of bent DNA segments by the structural property that causes rapid migration

Intrinsic DNA curvature is speculated to be a common feature of all satellite DNA sequences and may aid in the tight winding of DNA in constitutive heterochromatin. Several satellite DNAs, however, show unusually rapid migration in non-denaturing polyacrylamide gels, which is just the opposite behavior of that shown by curved DNA structures. Employing bovine satellite I DNA monomer, we attempted to understand the molecular mechanism of 'rapid migration'. The phenomenon of rapid migration was temperature-dependent and to a small extent polyacrylamide-concentration-dependent. Physiological or near-physiological concentrations of Mg2+and Ca2+ions bent the rapid migrating DNA segment. Predominance of purine-purine base stacking over purine-pyrimidine in nucleotide sequence was strongly indicated to be the cause of the rapid migration. Furthermore, they seemed to be implicated in the formation of induced DNA bend. We also found that the satellite I monomer contains an intrinsic DNA curvature as do many other satellites. Heretofore, the rapid migration property has concealed the presence of curvature.

Characterization of DNA fragments that show anomalously rapid migration in non-denaturing polyacrylamide gels

Several DNA fragments that show anomalously rapid migration in nondenaturing polyacrylamide gels have been cloned from digests of bovine genomic DNA. Electrophoretic behaviors of these fragments were analyzed in detail under various conditions. The results indicated that these fragments may adopt non-B DNA conformation.